Re: [AMBER] Chloride ion atom type issue in tleap

From: David A Case <>
Date: Sun, 1 Aug 2021 21:41:09 -0400

On Sun, Aug 01, 2021, Aliakbartehrani Zahra wrote:
>I tried loading the atomic_ions.lib and different combinations of
>amber residue name and corresponding atom type for a chloride ion (CL/Cl-,
>Cl-/ Cl- and so on) in the pdb input file, but that doesn't seem to work
>and still there is an issue for reading chloride ion:

You can use the "desc" command in tleap to interrogate loaded libraries:

loadOff atomic_ions.lib
list # shows loaded units
desc CL.1

This will show that both the residue name and the atom name are "CL"
>FATAL: Atom .R<Cl- 700>.A<CL 2> does not have a type.

This looks like your PDB file has Cl- as the residue name, which is wrong.

Aside: ignore anything containing Cl-: these were included to have backwards
compatibility with very old files. The PDB/IUPAC standard for a chloride
ion is the CL/CL pair.


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Received on Sun Aug 01 2021 - 19:00:02 PDT
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